feat: Fix observation timestamps, refactor session management, and enhance worker reliability (#437)

* Refactor worker version checks and increase timeout settings

- Updated the default hook timeout from 5000ms to 120000ms for improved stability.
- Modified the worker version check to log a warning instead of restarting the worker on version mismatch.
- Removed legacy PM2 cleanup and worker start logic, simplifying the ensureWorkerRunning function.
- Enhanced polling mechanism for worker readiness with increased retries and reduced interval.

* feat: implement worker queue polling to ensure processing completion before proceeding

* refactor: change worker command from start to restart in hooks configuration

* refactor: remove session management complexity

- Simplify createSDKSession to pure INSERT OR IGNORE
- Remove auto-create logic from storeObservation/storeSummary
- Delete 11 unused session management methods
- Derive prompt_number from user_prompts count
- Keep sdk_sessions table schema unchanged for compatibility

* refactor: simplify session management by removing unused methods and auto-creation logic

* Refactor session prompt number retrieval in SessionRoutes

- Updated the method of obtaining the prompt number from the session.
- Replaced `store.getPromptCounter(sessionDbId)` with `store.getPromptNumberFromUserPrompts(claudeSessionId)` for better clarity and accuracy.
- Adjusted the logic for incrementing the prompt number to derive it from the user prompts count instead of directly incrementing a counter.

* refactor: replace getPromptCounter with getPromptNumberFromUserPrompts in SessionManager

Phase 7 of session management simplification. Updates SessionManager to derive
prompt numbers from user_prompts table count instead of using the deprecated
prompt_counter column.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* refactor: simplify SessionCompletionHandler to use direct SQL query

Phase 8: Remove call to findActiveSDKSession() and replace with direct
database query in SessionCompletionHandler.completeByClaudeId().

This removes dependency on the deleted findActiveSDKSession() method
and simplifies the code by using a straightforward SELECT query.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* refactor: remove markSessionCompleted call from SDKAgent

- Delete call to markSessionCompleted() in SDKAgent.ts
- Session status is no longer tracked or updated
- Part of phase 9: simplifying session management

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* refactor: remove markSessionComplete method (Phase 10)

- Deleted markSessionComplete() method from DatabaseManager
- Removed markSessionComplete call from SessionCompletionHandler
- Session completion status no longer tracked in database
- Part of session management simplification effort

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* refactor: replace deleted updateSDKSessionId calls in import script (Phase 11)

- Replace updateSDKSessionId() calls with direct SQL UPDATE statements
- Method was deleted in Phase 3 as part of session management simplification
- Import script now uses direct database access consistently

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* test: add validation for SQL updates in sdk_sessions table

* refactor: enhance worker-cli to support manual and automated runs

* Remove cleanup hook and associated session completion logic

- Deleted the cleanup-hook implementation from the hooks directory.
- Removed the session completion endpoint that was used by the cleanup hook.
- Updated the SessionCompletionHandler to eliminate the completeByClaudeId method and its dependencies.
- Adjusted the SessionRoutes to reflect the removal of the session completion route.

* fix: update worker-cli command to use bun for consistency

* feat: Implement timestamp fix for observations and enhance processing logic

- Added `earliestPendingTimestamp` to `ActiveSession` to track the original timestamp of the earliest pending message.
- Updated `SDKAgent` to capture and utilize the earliest pending timestamp during response processing.
- Modified `SessionManager` to track the earliest timestamp when yielding messages.
- Created scripts for fixing corrupted timestamps, validating fixes, and investigating timestamp issues.
- Verified that all corrupted observations have been repaired and logic for future processing is sound.
- Ensured orphan processing can be safely re-enabled after validation.

* feat: Enhance SessionStore to support custom database paths and add timestamp fields for observations and summaries

* Refactor pending queue processing and add management endpoints

- Disabled automatic recovery of orphaned queues on startup; users must now use the new /api/pending-queue/process endpoint.
- Updated processOrphanedQueues method to processPendingQueues with improved session handling and return detailed results.
- Added new API endpoints for managing pending queues: GET /api/pending-queue and POST /api/pending-queue/process.
- Introduced a new script (check-pending-queue.ts) for checking and processing pending observation queues interactively or automatically.
- Enhanced logging and error handling for better monitoring of session processing.

* updated agent sdk

* feat: Add manual recovery guide and queue management endpoints to documentation

---------

Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>

src/services/worker/http/routes/SessionRoutes.ts

@@ -33,7 +33,6 @@ export class SessionRoutes extends BaseRouteHandler {
     super();
     this.completionHandler = new SessionCompletionHandler(
       sessionManager,
-      dbManager,
       eventBroadcaster
     );
   }
@@ -72,7 +71,6 @@ export class SessionRoutes extends BaseRouteHandler {
     app.post('/api/sessions/init', this.handleSessionInitByClaudeId.bind(this));
     app.post('/api/sessions/observations', this.handleObservationsByClaudeId.bind(this));
     app.post('/api/sessions/summarize', this.handleSummarizeByClaudeId.bind(this));
-    app.post('/api/sessions/complete', this.handleSessionCompleteByClaudeId.bind(this));
   }
 
   /**
@@ -286,7 +284,7 @@ export class SessionRoutes extends BaseRouteHandler {
 
     // Get or create session
     const sessionDbId = store.createSDKSession(claudeSessionId, '', '');
-    const promptNumber = store.getPromptCounter(sessionDbId);
+    const promptNumber = store.getPromptNumberFromUserPrompts(claudeSessionId);
 
     // Privacy check: skip if user prompt was entirely private
     const userPrompt = PrivacyCheckValidator.checkUserPromptPrivacy(
@@ -353,7 +351,7 @@ export class SessionRoutes extends BaseRouteHandler {
 
     // Get or create session
     const sessionDbId = store.createSDKSession(claudeSessionId, '', '');
-    const promptNumber = store.getPromptCounter(sessionDbId);
+    const promptNumber = store.getPromptNumberFromUserPrompts(claudeSessionId);
 
     // Privacy check: skip if user prompt was entirely private
     const userPrompt = PrivacyCheckValidator.checkUserPromptPrivacy(
@@ -390,31 +388,6 @@ export class SessionRoutes extends BaseRouteHandler {
     res.json({ status: 'queued' });
   });
 
-  /**
-   * Complete session by claudeSessionId (cleanup-hook uses this)
-   * POST /api/sessions/complete
-   * Body: { claudeSessionId }
-   *
-   * Marks session complete, stops SDK agent, broadcasts status
-   */
-  private handleSessionCompleteByClaudeId = this.wrapHandler(async (req: Request, res: Response): Promise<void> => {
-    const { claudeSessionId } = req.body;
-
-    if (!claudeSessionId) {
-      return this.badRequest(res, 'Missing claudeSessionId');
-    }
-
-    const found = await this.completionHandler.completeByClaudeId(claudeSessionId);
-
-    if (!found) {
-      // No active session - nothing to clean up (may have already been completed)
-      res.json({ success: true, message: 'No active session found' });
-      return;
-    }
-
-    res.json({ success: true });
-  });
-
   /**
    * Initialize session by claudeSessionId (new-hook uses this)
    * POST /api/sessions/init
@@ -440,8 +413,9 @@ export class SessionRoutes extends BaseRouteHandler {
     // Step 1: Create/get SDK session (idempotent INSERT OR IGNORE)
     const sessionDbId = store.createSDKSession(claudeSessionId, project, prompt);
 
-    // Step 2: Increment prompt counter
-    const promptNumber = store.incrementPromptCounter(sessionDbId);
+    // Step 2: Get next prompt number from user_prompts count
+    const currentCount = store.getPromptNumberFromUserPrompts(claudeSessionId);
+    const promptNumber = currentCount + 1;
 
     // Step 3: Strip privacy tags from prompt
     const cleanedPrompt = stripMemoryTagsFromPrompt(prompt);